You essentially need to organize it how you can use it best. When I started, I read somewhere that you should organize by type, all backgrounds, with folders of different colors, all frames in a folder, all word art in another, etc. Well I found that way doesn't work. You will find dozens of kits with files having the same name. You can only find new names for so many blue_clip.png's. And then I also started doing challenges, and several sites require you to use their products in their challenges, and this made it very very very hard to find things.
What I do now, is I have folders with the major scrap sites and also a folder for Bloggers. Under each site's folder, I have folders for each designer and then in that folder I have a folder for each kit. This way I tend to use items in a single kit more then I did before, but such is life. This way is much easier to credit your work, since you should always note who designs each piece on your layouts, in case you upload it down the road. It is proper etiquette to give proper credit.
I want to get ACDSee Photo Manager, with it you can put labels on your files and even if they are all in designer folders, you can do a search on blue clips and they will come up that way.